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Carr SM. Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera). Sci Rep 2023; 13:9386. [PMID: 37296293 PMCID: PMC10256785 DOI: 10.1038/s41598-023-35937-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a meta-analysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clock-calibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~ 780 Kya, and expansion to Southeast Europe and Asia Minor ~ 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa ~ 540 Kya. An African clade re-established in Iberia ~ 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of mis-referral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies.
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Affiliation(s)
- Steven M Carr
- Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL, A1C 5S9, Canada.
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Moškrič A, Marinč A, Ferk P, Leskošek B, Mosbech MB, Bunikis I, Pettersson OV, Soler L, Prešern J. The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies. Insects 2022; 13:insects13050403. [PMID: 35621738 PMCID: PMC9146700 DOI: 10.3390/insects13050403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary The western honeybee, Apis mellifera, is a globally distributed bee species with many recognised subspecies, one of which is Apis mellifera carnica, the Carniolan honeybee. Apis m. carnica is native to southern Central Europe and parts of the Balkans, with the locus classicus in Slovenia. It is also widely popular with beekeepers in parts of Central and Northern Europe and other parts of the world, including the USA, Canada, and even New Zealand. In Slovenia, A. m. carnica is protected, with measures to conserve the subspecies’ autochthonous domestic population in place. Such efforts depend heavily upon genomic and phylogenetic information. In this study, we sequenced and annotated the mitochondrial genome of a specimen from Slovenia and compared the obtained data with a previously published sample of the A. m. carnica from Austria and the closely related Italian honeybee A. m. ligustica. We found several features unique to the new mitochondrial genome. We also phylogenetically analyzed the relationship between our sequence and the selected available A. mellifera mitochondrial sequences. The acquired position of the sequenced A. m. carnica from Slovenia on the phylogenetic tree brings new evidence for close relationships among C and O lineages and reflects their recent historical matrilinear ancestry. Abstract The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.
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Affiliation(s)
- Ajda Moškrič
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
- Correspondence:
| | - Andraž Marinč
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
| | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/Centre ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia; (P.F.); (B.L.)
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/Centre ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia; (P.F.); (B.L.)
| | - Mai-Britt Mosbech
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, 751 24 Uppsala, Sweden;
| | - Janez Prešern
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
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Dogantzis KA, Tiwari T, Conflitti IM, Dey A, Patch HM, Muli EM, Garnery L, Whitfield CW, Stolle E, Alqarni AS, Allsopp MH, Zayed A. Thrice out of Asia and the adaptive radiation of the western honey bee. Sci Adv 2021; 7:eabj2151. [PMID: 34860547 PMCID: PMC8641936 DOI: 10.1126/sciadv.abj2151] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world’s most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic “hotspots.” We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.
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Affiliation(s)
- Kathleen A. Dogantzis
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Tanushree Tiwari
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Ida M. Conflitti
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Alivia Dey
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Harland M. Patch
- Department of Entomology, The Pennsylvania State University, State College, PA, USA
| | - Elliud M. Muli
- Department of Life Science, South Eastern Kenya University (SEKU), P.O. Box 170-90200, Kitui, Kenya
| | - Lionel Garnery
- Laboratoire Evolution Génome Comportement Ecologie (EGCE) UMR 9191, Gif sur-Yvette, France
| | - Charles W. Whitfield
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eckart Stolle
- LIB–Leibniz Institute for the Analysis of Biodiversity Change Museum Koenig, Center of Molecular Biodiversity Research Adenauerallee 160, 53113 Bonn, Germany
| | - Abdulaziz S. Alqarni
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Michael H. Allsopp
- Plant Protection Research Institute, Agricultural Research Council, Stellenbosch, South Africa
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
- Corresponding author.
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Abou-Shaara HF, Al-Ghamdi AA, Khan KA, Al-Kahtani SN. Genetic network analysis between Apis mellifera subspecies based on mtDNA argues the purity of specimens from North Africa, the Levant and Saudi Arabia. Saudi J Biol Sci 2021; 28:2718-2725. [PMID: 34025158 PMCID: PMC8117108 DOI: 10.1016/j.sjbs.2021.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/27/2022] Open
Abstract
Objectives This study aimed to analyze the genetic relationships between honey bee subspecies using reference specimens and recently collected specimens from different parts of the world. The purity of these specimens was discussed in light of the obtained results. Methods The genetic networks were constructed between 21 subspecies of honey bees, Apis mellifera L.: 9 in Africa, 7 in Europe and 5 in Asia. The analysis was performed using the mtDNA of these subspecies and the Population Analysis with Reticulate Trees software. Some subspecies were represented by more than two specimens based on the available online sequences. Results and conclusions The subspecies A. m. sahariensis from Africa showed unique characteristics and is genetically isolated than all other studied bee subspecies. Specimens collected from Saudi Arabia showed genetic relatedness to A. m. jemenitica, A. m. lamarckii, and some European subspecies, suggesting high degree of hybridization. The close genetic relationship between the Egyptian bees, A. m. lamarckii, and the Syrian bees, A. m. syriaca, were emphasized. The overall genetic network showed the presence of three distinct branches in relation to geographical locations. The high accurateness of the used analysis was confirmed by previous phylogenetic studies as well as the genetic relationships between hybrid bees of A. m. capensis and A. m. scutellata. The genetic networks showed the presence of bee subspecies from Africa in all branches including Europe and Asia. The study suggests the impurity of some specimens mostly due to the hybridization between subspecies. Specific recommendations for future conservation efforts of bees were presented in light of this study.
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Affiliation(s)
- Hossam F Abou-Shaara
- Department of Plant Protection, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Ahmad A Al-Ghamdi
- Chair of Engineer Abdullah Ahmad Buqshan for Bee Research, Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalid Ali Khan
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Saad N Al-Kahtani
- Arid Land Agriculture Department, College of Agricultural Sciences & Foods, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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Tihelka E, Cai C, Pisani D, Donoghue PCJ. Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera). Sci Rep 2020; 10:14515. [PMID: 32884034 PMCID: PMC7471700 DOI: 10.1038/s41598-020-71393-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022] Open
Abstract
Western honey bees (Apis mellifera) are one of the most important pollinators of agricultural crops and wild plants. Despite the growth in the availability of sequence data for honey bees, the phylogeny of the species remains a subject of controversy. Most notably, the geographic origin of honey bees is uncertain, as are the relationships among its constituent lineages and subspecies. We aim to infer the evolutionary and biogeographical history of the honey bee from mitochondrial genomes. Here we analyse the full mitochondrial genomes of 18 A. mellifera subspecies, belonging to all major lineages, using a range of gene sampling strategies and inference models to identify factors that may have contributed to the recovery of incongruent results in previous studies. Our analyses support a northern African or Middle Eastern origin of A. mellifera. We show that the previously suggested European and Afrotropical cradles of honey bees are the result of phylogenetic error. Monophyly of the M, C, and O lineages is strongly supported, but the A lineage appears paraphyletic. A. mellifera colonised Europe through at least two pathways, across the Strait of Gibraltar and via Asia Minor.
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Affiliation(s)
- Erik Tihelka
- Department of Animal Science, Hartpury College, Hartpury, GL19 3BE, UK.
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, 210008, China.
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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